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- PDB-7f49: von Willebrand factor (VWF) A1 domain with BT-100 aptamer RNA -

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Basic information

Entry
Database: PDB / ID: 7f49
Titlevon Willebrand factor (VWF) A1 domain with BT-100 aptamer RNA
Components
  • BT-100
  • von Willebrand factor
KeywordsBLOOD CLOTTING / aptamers / arterial thrombosis / platelets / primates / von Willebrand factor
Function / homology
Function and homology information


Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Defective VWF binding to collagen type I / Weibel-Palade body / Defective F8 binding to von Willebrand factor / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen ...Enhanced cleavage of VWF variant by ADAMTS13 / Defective VWF cleavage by ADAMTS13 variant / Defective VWF binding to collagen type I / Weibel-Palade body / Defective F8 binding to von Willebrand factor / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / hemostasis / platelet alpha granule / Platelet Adhesion to exposed collagen / positive regulation of intracellular signal transduction / GP1b-IX-V activation signalling / p130Cas linkage to MAPK signaling for integrins / cell-substrate adhesion / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / immunoglobulin binding / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin cell surface interactions / collagen binding / Intrinsic Pathway of Fibrin Clot Formation / Integrin signaling / extracellular matrix / platelet alpha granule lumen / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet activation / response to wounding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / blood coagulation / integrin binding / Platelet degranulation / protein-folding chaperone binding / collagen-containing extracellular matrix / protease binding / cell adhesion / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
von Willebrand factor, VWA N-terminal domain / Von Willebrand factor / VWA N-terminal / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain ...von Willebrand factor, VWA N-terminal domain / Von Willebrand factor / VWA N-terminal / C8 domain / Uncharacterised domain, cysteine-rich / C8 / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain / C-terminal cystine knot signature. / von Willebrand factor (vWF) type C domain / Trypsin Inhibitor-like, cysteine rich domain / Serine protease inhibitor-like superfamily / Trypsin Inhibitor like cysteine rich domain / C-terminal cystine knot domain profile. / Cystine knot, C-terminal / C-terminal cystine knot-like domain (CTCK) / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / von Willebrand factor (vWF) type C domain / VWFC domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / von Willebrand factor
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsZhu, S.
CitationJournal: J Thromb Haemost. / Year: 2020
Title: The development and characterization of a long acting anti-thrombotic von Willebrand factor (VWF) aptamer
Authors: Zhu, S. / Gilbert, C.J.
History
DepositionJun 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: von Willebrand factor
B: BT-100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1213
Polymers34,0292
Non-polymers921
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.980, 122.404, 42.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-879-

HOH

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Components

#1: Protein von Willebrand factor / / vWF


Mass: 24020.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VWF, F8VWF / Production host: Escherichia coli (E. coli) / References: UniProt: P04275
#2: DNA chain BT-100


Mass: 10008.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M Sodium Acetate pH 4.6, 18% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97894 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97894 Å / Relative weight: 1
ReflectionResolution: 2.09→44.59 Å / Num. obs: 19318 / % possible obs: 92.5 % / Redundancy: 6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.021 / Rrim(I) all: 0.052 / Net I/σ(I): 21.3
Reflection shellResolution: 2.09→2.2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.391 / Num. unique obs: 2840 / CC1/2: 0.884 / Rpim(I) all: 0.219 / Rrim(I) all: 0.452 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimless0.7.2data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SQ0

1sq0


Resolution: 2.09→44.55 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 10.92 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.238 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2388 973 5.1 %RANDOM
Rwork0.2074 ---
obs0.209 18243 92.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.62 Å2 / Biso mean: 46.071 Å2 / Biso min: 26.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å2-0 Å2-0 Å2
2---0.82 Å20 Å2
3---1.57 Å2
Refinement stepCycle: final / Resolution: 2.09→44.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1596 668 6 124 2394
Biso mean--53.11 47.34 -
Num. residues----228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0152379
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182010
X-RAY DIFFRACTIONr_angle_refined_deg1.9452.0233344
X-RAY DIFFRACTIONr_angle_other_deg1.0711.8564632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1925199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.8620.76991
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89415311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7111516
X-RAY DIFFRACTIONr_chiral_restr0.0670.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022170
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02545
LS refinement shellResolution: 2.09→2.14 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.34 67 -
Rwork0.32 1304 -
obs--91.4 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.1025-0.2287-0.89542.83710.05653.42960.10790.19490.426-0.07540.02040.2163-0.2167-0.4054-0.12830.02370.02450.020.05160.02770.0965-17.39658.9438-19.2627
20.65330.444-0.09893.9441.92591.2573-0.26280.0824-0.40880.14750.2413-0.17690.4270.13360.02150.42720.02210.03250.1641-0.0080.3472-9.0011-18.5784-18.8855
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A505 - 702
2X-RAY DIFFRACTION2B1 - 30

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